R Workshop

Module 6: “To Infinity and Beyond” (1)

2018-04-18
Bobae Kang
(Bobae.Kang@illinois.gov)

Source: R Markdown

“R Markdown is a file format for making dynamic documents with R. An R Markdown document is written in markdown (an easy-to-write plain text format) and contains chunks of embedded R code.”

- Garret Grolemund from R Studio

• Reproducible
• Multiple document formats
• Embedding R code chunks (and the outputs)

• Install rmarkdown
  • not necessary if using R Studio IDE
• Create a R markdown document
  • File > New File > R Markdown
• “Knit” the R markdown document into a file in the desired format

• YAML header
• knit and preview outputs
• markdown
• code chucks

• Title, author, date
• output
  • output format
  • output options
  • different output format has different options

• Headers
• Font types (italic, bold, strikethrough, superscript)
• Lists (ordered, unordered)
• Hyperlinks
• Images
• Blackquotes
• Horizontal line/page break
• Math equations (using LaTeX)
• Code/R code (chunk, in-line)

• Global options
  • Act as the default settings for the whole document
• Local options (per code chunk)
  • Only applied to the specific code chunck
  • Overide the global options if relevant

• Insert images with knitr::include_graphics()
• Image size
• Image alignment

• Printing basic data frame object
• Better looking tables with knitr::kable()
• Interactive tables with DT::datatable()

Source: Wikimedia Commons

---
title: "My first R Markdown document"
output: html_document
---

---
title: "My first R Notebook"
output: html_notebook
---

“An R Notebook is an R Markdown document with chunks that can be executed independently and interactively, with output visible immediately beneath the input.”
- “R Notebooks”, RStudio

• Thera are many R packages (90+) for taking full advantage of the interactivity that web can offer.
• With these packages, we can easily incorporate interactive widgets into HTML documents generated using R Markdown
• Examples of htmlwidgets include:
  • plotly and highcharter for interactive visualizations
  • leaflet for interactive maps
  • DT for interactive data tables
• Visit htmlwidgets for R website to find out more

---
title: "My PDF document"
output: pdf_document
---

---
title: "My word document"
output: word_document
---

• d
• d
• d

“RPubs is a quick and easy way to disseminate data analysis and R code and do ad-hoc collaboration with peers.”
- RStudio Team

• Publishing an R Markdown output on RPubs is as easy as clicking the “publish” button on RStudio
• Comparable to Tableau Public's Gallery website(?)

Source: Wikimedia Commons

• RStudio supports many ways to create presentation slides that are both modern-looking and highly customizable
• Popular ways to create slides using R include:
  • R Markdown formats:
    • ioslides_presentation (HTML)
    • revealjs::revealjs_presentation (HTML)
    • slidy_presentation (HTML)
    • beamer_presentation (PDF)
  • R Presentation (HTML)

---
title: "My first ioslide presentation"
output: ioslides_presentation
---

• ioslides output format is built into RStudio
• Fully integrates R Markdown syntax
  • Creating new slides is as easy as using # and ## headings
• To learn more about ioslides, read the “Presentations with ioslides” article on RStudio

---
title: "My first revealjs presentation"
output: revealjs::revealjs_presentation
---

• With revealjs R package, it is possible to use R Markdown (and its syntax) to generate slides using reveal.js, a JavaScript library for interactive slides in HTML
  • Try this demo slides generated using reveal.js
• To learn more about revealjs, read the “Presentations with reveal.js” article on RStudio

• HTML presentations with slidy
  • Use output: slidy_presentation in the YAML header
  • See the “Presentations with Slidy” article on RStudio
• PDF presentations with beamer
  • Use output: beamer_presentation
  • See the “Presentations with Beamer” article on RStudio
• HTML presentations with xaringan
  • Use output: xaringan::moom_reader
  • Visit the package GitHub repository for more

• Not a R Markdown document
• All ICJIA R Workshop slides are generated using R Presentation
• To learn more R Presentation, visit relevant pages on RStudio Support website

Source: R Studio

“Shiny is an open source R package that provides an elegant and powerful web framework for building web applications using R. Shiny helps you turn your analyses into interactive web applications without requiring HTML, CSS, or JavaScript knowledge.”
- RStudio.com

• Check out my ICJIA UCR Data dashboard app here
• Check out more examples on RStudio's “Shiny User Showcase” page

• A data dashboard is a visual interface to data to allow its viewers for gain key insights
• It is often an interactive application that provides viewers with options to explore data from multiple angles interactively
• Shiny application can make a great dashboard

• Shiny can be used to generate interactive documents with Shiny app widgets
• An interactive document is an R Markdown file with the YAML head including runtime: shiny and output: html_document or output: ioslids_presentation

Source: Wikimedia Commons

• A collection R Markdown documents in HTML format can be made into a website
  • To do so, we need a _site.yml file in the same folder as individual documents to be put together
  • _site.yml specifies the name and the routing structure of the resulting website
  • With _site.yml and all HTML documents ready, run rstudio::render_site() to generate the website
• For details, see the “R Markdown Websites” article on RStudio website

“GitHub Pages is a static site hosting service designed to host your personal, organization, or project pages directly from a GitHub repository.”
-“What is GitHub Pages?”, GitHub Help

• GitHub is a free and commercial online repository service for storing and sharing projects using Git
• The ICJIA R Workshop website is hosted on GitHub Pages
• Read more about GitHub Pages and hosting static sites on GitHub Pages on GitHub Help here

• bookdown package, built on R Markdown, facilitates writing books and long articles/reports.
  • A bookdown publication is made downloadable in PDF, EPUB and MOBI formats
• Check out bookdown package website to find out more
• Also, read Xie, Y. (2018). bookdown: Authoring Books and Technical Documents with R Markdown for a comprehensive guide for bookdown
  • The book itself is generated using bookdown

• blogdown is a package to generate static websites using R Markdown and the Hugo open-source framework for building websites
• Visit Awesome Blogdown website for a curated list of blogdown examples
• Also, read Xie, Y. et al. (2018). blogdown: Creating Websites with R Markdown for a comprehensive guide for blogdown

Source: Giphy